Primer Software?

[Sebastian Cocioba]

I use Primer 3 Plus. Its nice and simple. What are your favorites? Anyone ever try premier biosoft's program? Did anyone ever get Tm that's way off predicted? Just trying to get an idea of what everyone uses to see if im not missing out on some open source goodness. Thanks!

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D

[Koeng]

I use snapgenes built in software. Just outline dna and it gives TM. I highly recommend the trail version

[Sebastian Cocioba]

I have the licensed version for my company but I really don't trust the primer Tm calculation since it does not use the "latest" calculation methods. If you take your primer made via snapgene and plug it into a more sophisticated program like Primer 3 Plus, which checks for hairpins, self annealing, and a ton of other user editable parameters, the Tm will vary from program to program. I've had issues designing primers via snapgene's minimalistic calculation approach. A few of my longer primers ~40bp failed. Later analysis with Primer 3 Plus showed a high chance of hairpin. When I redesigned it using only primer 3 it worked like a charm. I absolutely LOVE SnapGene but its trying to be jack of all trades. Even though I get my primers for a flat $5 a pop, its still a waste to have them fail due to silly avoidable design flaws...partly my own fault :P

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D

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From: Koeng
Sent: 1/31/2014 11:27 AM
To: diy...@googlegroups.com
Subject: [DIYbio] Re: Primer Software?

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[Koeng]

Invitrogen value oligos ftw

I think its true that snapgene is trying to be the jack of all trades... I wish there was opensource software (hint hint) just like theirs so you could program your own plugins. So far all the free ones i have tried don't even marginally compare to it. On the topic of primers, I wish they added more support in for primers... last time I asked about it they gave this, which was pretty good explanation

-Koeng 

[Kevin Chen]

For open source stuff, there is this one: http://gentledna.org/

I think it might still need more development but it's a pretty good start, and it'll probably be good stuff other than PCR too. You can write plugins for it, but I'm not much of a programmer so I'm not sure what exactly that entails.

Link to the first version, for reference: http://gentle.magnusmanske.de/

Cheers,

Kevin

[Hugo Correia]

Actually didn't know about it. Seems to have good chances, just hope it grows in functionality. Proprietary software is too expensive for people who don't need everything.

[Cathal Garvey]

I used the original GENTLE (available by apt-get on Debian) to design my
first plasmid. It's pretty unstable these days, so it kept crashing and
losing work, but aside from that it's still pretty good software. My
only gripe is that it assumes traditional cloning, sort-of. That is,
modifying DNA at will is possible but the UI makes it slightly awkward
because it assumes you'll always be using restriction enzymes and PCR to
copy and paste existing DNA together; making arbitrary changes to DNA?
Unthinkable! :)

Still, good software, worth trying if you can tolerate the crashing.
Save regularly!

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[Hugo Correia]

I use Geneious as I get along very well with it, could be better for non-traditional cloning strategies but it's doable, though expensive. Snapgene is great to get plasmid libraries out of it :D.

[Brian Degger]

https://gentle.synbiota.com/ is a nice site too, for collaborating on dna sequences. 

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